Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparsion of OMV to membrane proteomes across different media (OMV vs membrane experiments)

ABSTRACT: This project examines the impact of different growth media on the protein compositions of OMV and membrane of Bacteroides thetaiotaomicron.

INSTRUMENT(S):

ORGANISM(S): Bacteroides Thetaiotaomicron

SUBMITTER: Nichollas Scott

LAB HEAD: Mario Feldman

PROVIDER: PXD036181 | Pride | 2023-06-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20211009_NSco-3118_Bt_Mem_Mannose_B1.raw	Raw
	20211009_NSco-3118_Bt_Mem_Mannose_B1_-45.mzXML	Mzxml
	20211009_NSco-3118_Bt_Mem_Mannose_B1_-65.mzXML	Mzxml
	20211009_NSco-3118_Bt_Mem_Mannose_B2.raw	Raw
	20211009_NSco-3118_Bt_Mem_Mannose_B2_-45.mzXML	Mzxml

Items per page:

1 - 5 of 157

Similar Datasets

Comparison of OMV to membrane proteomes across different media (OMV)

Project description:This project examines the impact of different growth media on the protein compositions of OMV and membrane of Bacteroides thetaiotaomicron.

2023-06-14 | PXD036275 | Pride

Comparison of OMV to membrane proteomes across different media (membrane experiments)

Project description:This project examines the impact of different growth media on the protein compositions of membranes of Bacteroides thetaiotaomicron.

2023-06-14 | PXD036272 | Pride

Bacteroides thetaiotaomicron OMV proteomics

Project description:Comparative proteomics of Bacteroides thetaiotaomicron samples comparing the total membrane (TM) and outer membrane vesicles (OMV) of WT B. thetaiotaomicron and delta 4364

2024-10-15 | PXD043219 | Pride

Combining FAIMS based Glycoproteomic and DIA Proteomic of reveals widespread proteome alteration in response to changes in N. gonorrhoeae glycosylation.- FAIMS pglO alleles

Project description:Protein glycosylation is increasingly recognized as a common protein modification across bacterial species. Within members of the Neisseria genus O-linked protein glycosylation plays important roles in virulence and antigenic variation yet our understanding of the substrates of glycosylation are limited. Recently it was identified that even closely related Neisserial species can possess O-oligosaccharyltransferases, pglOs, that possess varying glycosylation specificities suggesting that distinct targeting activities may impact both the glycoprotome as well as the proteome of Neisserial species. Within this work we explore this concept using of Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) fractionation and Data-Independent Acquisition (DIA) to allow the characterization of differences in the glycoproteomes and proteomes within N. gonorrhoeae strains expressing differing pglO alleles. We demonstrate the utility of FAIMS to expand the known glycoproteome of N. gonorrhoeae and enable comparative glycoproteomics of a recently reported panel of N. gonorrhoeae strains expressing different pglO allelic chimeras (15 pglO enzymes) with unique substrate targeting activities. Combining glycoproteomic insights with DIA proteomics we demonstrate that alterations within pglO alleles have widespread impacts on the proteome of N. gonorrhoeae yet lead to minimal effects on the abundance of glycoproteins. Additionally, while DIA analysis can allow occupancy to be inferred by the absence or presence of peptides known to be modified, we observe a poor correlation between DIA measurements of non-modified versions of glycopeptides and glycoproteomic analysis. Combined this work expands our understanding of the N. gonorrhoeae glycoproteome and supports that the expression of different pglO alleles appears to drive proteomic changes independent of the glycoproteins targeted for glycosylation.

2024-02-01 | PXD044666 | Pride

Combining FAIMS based Glycoproteomic and DIA Proteomic of reveals widespread proteome alteration in response to changes in N. gonorrhoeae glycosylation.

2024-02-01 | PXD044665 | Pride

Glycoproteomic and Proteomic analysis of Burkholderia cenocepacia reveals glycosylation events within FliF and MotB are dispensable for motility. -FAIMS Log growth

Project description:Within the Burkholderia genus O-linked protein glycosylation is now known to be highly conserved at the pathway and glycosylation substrate levels. While inhibition of glycosylation has been shown to be detrimental to virulence in B. cenocepacia, little is known about the role of glycosylation in Burkholderia glycoproteins. Within this study we have sought to improve our understanding of the breadth and dynamics of the B. cenocepacia O-glycoproteome to identify glycoproteins which require glycosylation for functionality. Assessing the glycoproteome across multiple common culturing media (LB, TSB, and artificial sputum medium to simulate cystic fibrosis sputum-like conditions) we demonstrate at least 141 glycoproteins are subjected to glycosylation within B. cenocepacia K56-2. Leveraging this insight, we quantitively assessed the glycoproteome of B. cenocepacia using Data-Independent Acquisition (DIA) across culturing media and growth phases revealing most B. cenocepacia glycoproteins are express under all conditions. Examination of how the absence of glycosylation impacts the glycoproteome reveals only a subset of the glycoproteome (BCAL1086, BCAL2974, BCAL0525, BCAM0505 and BCAL0127) appear impacted by the loss of glycosylation. Assessing the proteomic and phenotypic impacts of the loss of these glycoproteins compared to glycosylation null strains revealing the loss of BCAL0525, and to a lesser extend BCAL0127, mirror the proteomic effects observed in the absence of glycosylation. Finally, we demonstrate the loss of glycosylation within BCAL0525 at Serine-358 results in both loss of motility and proteomic impacts on flagellar apparatus consistent with the loss of apparatus stability. Combined this work demonstrates that O-linked glycosylation of BCAL0525 is functionally important within B. cenocepacia.

2024-04-17 | PXD043188 | Pride

Glycoproteomic and Proteomic analysis of Burkholderia cenocepacia reveals glycosylationevents within FliF and MotB are dispensable for motility. -FAIMS stationary growth

2024-04-17 | PXD043193 | Pride

neisserial OTases have different protein specificies

Project description:Proteomic investigation on the glycosylation substrates and proteome effects of altering neisserial OTases within the proteome of N. gonorrhoeae MS11

2022-04-04 | PXD024737 | Pride

CBU1543 immunopercipation (CBU1543 vs empty vector)

Project description:immunopercipation of CBU1543 to identify interaction partners

2023-08-07 | PXD030191 | Pride

Identification of levoglucosan degradation pathways in bacteria

Project description:Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degrading Paenarthrobacter spp. (Paenarthrobacter nitrojuajacolis LG01 and Paenarthrobacter histidinolovorans LG02) that were isolated by metabolic enrichment on levoglucosan as sole carbon source. Genome sequencing and proteomics analysis revealed expression of a series of gene clusters encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan b-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident. The expressed gene clusters contained a range of putative sugar phosphate isomerase/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbors revealed that homologues of LgdA, LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One sugar phosphate isomerase/xylose isomerase cluster (LgdB3) was identified with limited distribution mutually exclusive with LgdB2. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight the diversity within the LGDH pathway through which bacteria utilize levoglucosan as a nutrient source.

2023-05-10 | PXD039086 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data